Is the Virus Mutating? Answers from Evolutionary Biologists

Since SARS-CoV-2 was first detected in late 2019, fears and rumors of new, deadlier strains of the virus seem to fill the news. We speak with Dr. Erik Wright and Dr. Vaughn Cooper, evolutionary biologists and professors at the University of Pittsburgh, on the SARS-CoV-2 mutation and its potential impacts on the pandemic.

We’ve all heard worries about virus mutation and new strains of SARS-CoV-2, the virus that causes COVID-19. A recent study, awaiting peer-review, looked into mutations of the Spike (S) protein that is used to invade cells and suggests the emergence of a more transmissible form of the virus.

But not all scientists agree. While there is still a lot of uncertainty surrounding COVID-19, scientists have published an article debunking panicked fears of virus mutations, emphasizing that “mutations are a natural part of the virus life cycle and rarely impact outbreaks dramatically.” Dr. Erik Wright and Dr. Vaughn Cooper, two evolutionary biologists and professors at the University of Pittsburgh, also recently produced a video to clarify on the topic of SARS-CoV-2 mutation.

The short story? Yes, COVID-19 “mutates,” like all other viruses. But it seems it’s not mutating enough to cause different strains at this time and, actually, these smaller mutations can help scientists genetically track and identify where COVID-19 is spreading from. But that doesn’t mean it couldn’t eventually be a problem; once a vaccine is developed we may see more specific mutations and selection processes that work to evade the vaccine.

“[T]he virus is actually mutating more slowly than we expect,” Wright said. “[F]rom the science perspective, [what] we see is that the virus actually doesn’t seem to be mutating very rapidly and there’s absolutely no basis for saying that there [are] multiple strains of this virus at the moment.”

Then what mutation does or doesn’t constitute a new strain? There can be mutations that introduce small changes in the genetic sequence of a virus, but do not greatly alter the virus in a way to define a new strain. Cooper said that this particular virus is able to keep its mutation rate low because of a fairly unique ability of coronaviruses, called proofreading, that reduce errors when replicating their genetic material.

What determines what mutations will be carried on?

“When a virus mutates, that doesn’t mean that that mutation gets passed on. In order for the mutation to be passed on, it has to either be lucky and get passed on, or it has to be adaptive and so increase in abundance faster than the ancestor,” Wright said. “And accepting the mutation means that the virus is ‘happy’ that it did that, and that mutation increases in abundance because it’s an advantageous thing to have done.”

Still, mutations, albeit slow, are happening and can actually be helpful in tracking the history and spread of the virus.

“There were a few sort of diagnostic early changes in the virus—again, not likely changing the virus in a significant way that affects how virulent it is—but they provide markers—fingerprints—of where they were,” Cooper said.

Scientists are able to use these markers to identify similar mutations in virus genomes and trace the lineage of its spread; the origin of a majority of COVID-19 cases on the East and West Coasts have been linked back to Europe and Asia, respectively.

At this stage, as we are awaiting a vaccine, the virus will continue to spread and mutations will be random and slow. While some have feared that virus mutations could make current vaccine research ineffective, some scientists argue it most likely won’t be a problem.

“On average, any two viruses that you sample from around the world differ by […] only seven or so positions of 30,000, and those seven or so positions are not in areas of the virus that are likely to be part of the vaccine strategy. You can basically design one vaccine and […] those little, but subtle variations are not gonna factor [into] that vaccine strategy,” Cooper said.

It’s after the use of a vaccine where two problems come in. The first relates to the period of immunity that vaccines may offer. The CDC provides recommendations on vaccines; some require repeated application to provide protection from diseases like influenza or tetanus, diphtheria and pertussis (Tdap).

“The adaptive immune system will acquire immunity and then that immunity can wane over time and I think that’s one of the big question marks,” Wright said, using SARS as an example.

“So if you get SARS today and your adaptive immune system acquires immunity to it, how many years later could you be challenged with SARS and still be immune to it? And that might be one, that might be ten, that might be your entire life and that varies depending on the virus,” he said.

The second of these issues is related to the virus itself and its response to the vaccine.

“Once you deliver that vaccine, then selection happens. Selection for viruses that evade that vaccine response will be strong. And so we would be looking immediately for using the genomes of those viruses to see if selection is favoring particular variants that are morphed in spite of an active vaccine-induced immune response,” Cooper said.

So, on some level, mutations can be dangerous. But for the most part and for our current situation, Cooper and Wright argue that virus mutations and adaptation are normal processes. The variation we see in symptoms today speaks more to the diversity of responses of the human body in different people, making us reconsider how we move ahead.

“This virus, it’s basically all the same virus, but look at the really wide range of responses that we have to this one virus. I think that teaches us a lot about how we have to acknowledge our own variation and be aware of it and think about how to to mitigate those risks,” Cooper said.

While we are consulting experts in the field to get answers to important questions during this crisis, new information and studies come out almost every day and much remains unknown regarding COVID-19. Midstory encourages everyone to follow all public health and safety protocols and exercise extreme caution.

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